HSPA4

heat shock protein family A (Hsp70) member 4, the group of Heat shock 70kDa proteins

Basic information

Region (hg38): 5:133052013-133106449

Links

ENSG00000170606 ∙ NCBI:3308 ∙ OMIM:601113 ∙ HGNC:5237 ∙ Uniprot:P34932 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the HSPA4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the HSPA4 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous					4	4
missense			27	1	2	30
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1	1	2
non coding					1	1
Total	0	0	27	1	7

Variants in HSPA4

This is a list of pathogenic ClinVar variants found in the HSPA4 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
5-133052346-C-T			Benign (Mar 29, 2018)
5-133067442-T-C		not specified	Uncertain significance (Aug 15, 2023)
5-133067465-G-C		not specified	Uncertain significance (Apr 26, 2024)
5-133067510-C-T		not specified	Uncertain significance (Jul 10, 2024)
5-133070378-C-A		not specified	Likely benign (Jan 19, 2024)
5-133070383-A-T		not specified	Uncertain significance (Mar 02, 2023)
5-133070408-C-T		not specified	Uncertain significance (May 29, 2024)
5-133073253-A-G			Benign (Apr 20, 2018)
5-133073311-A-T		not specified	Uncertain significance (Jul 05, 2024)
5-133073328-A-G			Likely benign (May 18, 2018)
5-133074057-A-C			Benign (Dec 31, 2019)
5-133076650-T-A			Benign (Apr 06, 2018)
5-133076676-C-T		not specified	Uncertain significance (Aug 02, 2022)
5-133076816-T-C			Benign (Jan 05, 2018)
5-133076819-A-T		not specified	Uncertain significance (Dec 13, 2022)
5-133086805-A-G		not specified	Uncertain significance (May 30, 2024)
5-133086842-T-G		not specified	Uncertain significance (Aug 09, 2021)
5-133089080-A-G		not specified	Uncertain significance (Oct 29, 2024)
5-133089154-G-C		not specified	Uncertain significance (Jun 26, 2024)
5-133089154-G-T		not specified	Uncertain significance (May 17, 2023)
5-133089579-C-G		not specified	Uncertain significance (May 30, 2023)
5-133089594-C-T		not specified	Uncertain significance (Apr 24, 2024)
5-133089609-T-C		not specified	Uncertain significance (Nov 08, 2024)
5-133089621-A-G		not specified	Uncertain significance (Mar 23, 2023)
5-133092706-C-G		not specified	Uncertain significance (Aug 08, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
HSPA4	protein_coding	protein_coding	ENST00000304858	19	54488

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.000463	125631	0	116	125747	0.000461

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.06	311	431	0.721	0.0000207	5549
Missense in Polyphen		106	193.41	0.54806		2477
Synonymous	-0.486	156	148	1.05	0.00000711	1505
Loss of Function	5.66	6	48.5	0.124	0.00000284	583

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000256	0.000185
Ashkenazi Jewish	0.00271	0.00119
East Asian	0.000610	0.000326
Finnish	0.00103	0.000508
European (Non-Finnish)	0.00138	0.000686
Middle Eastern	0.000610	0.000326
South Asian	0.0000415	0.0000327
Other	0.00181	0.000815

dbNSFP

Source: dbNSFP

• Pathway: Antigen processing and presentation - Homo sapiens (human);Tight junction - Homo sapiens (human);Glucocorticoid Pathway (Peripheral Tissue), Pharmacodynamics;Parkin-Ubiquitin Proteasomal System pathway;Regulation of HSF1-mediated heat shock response;Cellular responses to stress;AndrogenReceptor;Cellular responses to external stimuli;Cellular response to heat stress;Validated targets of C-MYC transcriptional activation (Consensus)

Recessive Scores

• pRec: 0.952

Intolerance Scores

• loftool: 0.407
• rvis_EVS: -0.15
• rvis_percentile_EVS: 42.23

Haploinsufficiency Scores

• pHI: 0.983
• hipred: Y
• hipred_score: 0.853
• ghis: 0.640

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.909

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Hspa4
• Phenotype: cellular phenotype; endocrine/exocrine gland phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); reproductive system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan)

Gene ontology

• Biological process: response to unfolded protein;protein insertion into mitochondrial outer membrane;chaperone-mediated protein complex assembly
• Cellular component: nucleus;cytosol;extracellular exosome
• Molecular function: protein binding;ATP binding